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Think I've got my ClawdBot just about dialed in 9:47 AM - "hey clawdbot" 9:47 AM - Clawdbot: "hey, what's up" 9:48 AM - "thinking about building a tax automation tool" 9:48 AM - Clawdbot: "Got it. Incorporating LLC. EIN pending. Domain obtained." 9:49 AM - "wait no I was…
Eyes wide open!
So 2025 turned out to be a big year for de novo antibody design! Here are thoughts and predictions on the state of de novo antibody design heading into 2026 🧵
This is what amino acids look like if you let the side chains flop around on the page
I wouldn't say "mapping". It also works on new MSAs it never seen before. What it really learned was how to extract contacts (graph) from a multiple sequence alignment (MSA), filter it and and embed it in 3D space.
But here's where things get slippery: The FDA defines "proteins" as sequences of alpha-amino acids that are *greater* than 40 amino acids long. Proteins are considered biologics by the FDA. Retatrutide, however, is exactly 39 alpha-amino acids (plus a linker). They're literally…
Latest @ChemRxiv preprint! "Scalable Low-Energy Molecular Conformer Generation with Quantum Mechanical Accuracy" Collaboration w/ @NVIDIAHealth We created ChEMBL3D, largest dataset of molecular 3D structures with 250M+ conformers for 1.8M drug-like molecules from ChEMBL. All…
New @Nature The possibility that lithium deficiency is a driver of Alzheimer's disease. Experimental model shows Li depletion impedes amyloid clearance, and repletion in humans could be achieved with low doses nature.com/articles/s4158…
This is sad!
CASP is getting cut by NIH... 😢 (Anyone with extra funds wanna help support perhaps the most important competition of the century?) science.org/content/articl…
It is very sad to learn that Martin Karplus passed away on Dec 28 at age 94. He was a scholar and pioneering chemical physicist with great contributions in many areas including molecular dynamics. We interacted many times starting from my graduate time at Harvard. His legacy is…
You may have seen a recent pre-print [1] from Jain et al. with strongly worded claims against the experimental results in our DiffDock paper [2]. We initially declined to respond as we saw that this preprint contained falsehoods, misleading comparisons, seemingly deliberate…
Super excited to preprint our work on developing a Biomolecular Emulator (BioEmu): Scalable emulation of protein equilibrium ensembles with generative deep learning from @MSFTResearch AI for Science. #ML #AI #NeuralNetworks #Biology #AI4Science biorxiv.org/content/10.110…
Hitchhiker's guide to rebranding: - Machine learning -> statistical mechanics - Loss function -> energy functional - Optimize the model -> minimize free energy - Trained model -> reached equilibrium distribution - KL divergence -> free energy difference - Gaussian noise -> random…
So I was chatting with somebody who was showing me some structures, and he typed "set grid_mode,1" in pymol and it shows all the active objects in a grid, and they all rotate and move at the same time with the mouse. I was like, "I didn't know it could do that..."
EXPENSIVE THINGS IN DRUG DISCOVERY $100 per hour a scientist spends in lab $300 per assay plate (and just the plastic plate!) $1,000 per team meeting to decide what to do $3,000 per compound that actually gets made $10,000 to see if that compound is orally absorbed in…
Nonequilibrium physics rules the world. Here are eight chapters introducing key aspects of nonequilibrium biophysics illustrated with simple examples. osf.io/9yq2n/
Have you ever done a dense grid search over neural network hyperparameters? Like a *really dense* grid search? It looks like this (!!). Blueish colors correspond to hyperparameters for which training converges, redish colors to hyperparameters for which training diverges.
🚨🚨Fancy a 🤓 trip to NYC in May? Pls join @tamar_schlick & me at @SimonsCenterNYU for our Simons Symposium on ✨CHALLENGES IN BIOMOLECULAR SIMULATIONS✨ We are looking for more speakers from abstracts! wp.nyu.edu/sccpc/event/ch… Look at this lineup!! 🤩🤩🤩 Join us!
BREAKING NEWS The 2023 #NobelPrize in Physiology or Medicine has been awarded to Katalin Karikó and Drew Weissman for their discoveries concerning nucleoside base modifications that enabled the development of effective mRNA vaccines against COVID-19.
This is cool. Back in the day, @simmerling lab had thematic machine names that were different chilies 🌶️, the hottest being the most powerful 🔥
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